Modified create_dmri_preprocessing to allow for pipeline use with and without fieldmap files
 - Added use_fieldmap flag to create_dmri_preprocessing
Fixed error in _rotate_bvec that was adding an extra entry to the output rotated_bvecs file and offsetting the correction by one volume.

Noted that the first two entries in the rotated_bvec files were 0,0,0 when the bvalues of the first two files were 0 and 1000. Plotting the original bvec against the rotated bvec (X component) showed what appeared to be a single volume offset (see black and red traces in attached plot)

code issue:  _rotate_bvec code initialised its output bvec array with the first entry of the input bvec array and then looped through FLIRT matrices starting at 1st position, but used a 0-based index for selecting the input from the bvec array

solution    :  initialise output array filled with zeros, loop through FLIRT matrices from 0, use 0-based indexing for selecting input from the bvec array, set consecutive elements appropriately

testing      : nothing, other than plotting the X component for one subject
Merge pull request #543 from steelec/bug-fix_rotate_bvec

Bug fix rotate bvec